Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_017840
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 228493
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Found at i:52067 original size:12 final size:12
Alignment explanation
Indices: 52052--52085 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
52042 TAAAGGTATA
*
52052 TATATATATTAT
1 TATATATATTAG
52064 TATATATATTAG
1 TATATATATTAG
52076 TATATTATAT
1 TATA-TATAT
52086 ATATAATACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (12 bp):
TATATATATTAG
Left flanking sequence: Indices 51552 -- 52051
GATATTCTATGCATCTATGCAATTAGCAGTTGCTACTGCGCATTACTCACGACGTGGATGATAAC
CCTAACTGTCCCCTTATAGTGGATCGCGGGCTTTTCGGCTTGAAGTTTTGTAATCAATGAAGTCC
TGTCATGAAAAGAGGAAGTGTAACCTAATACAGAGACTTGTTGCGCACTTATTGAGTCGCTGCTC
AAATTGGTTGTGTGTGGTTATGACCTAAACTGCATAAAAACGATCGTTCTAGGCGCATTTAAAAG
CCTTTAAAAATAAAATGGTTTTTTTTCTCCTGTCTCATAATTCCGGTTTACTTTCAGTATGGGAT
CTTTATTTCTACTATTTTGTTTAAGTCTTTCTCGGTGTCCGGCTTGGGTTCGGGTTTGTCTGCTT
TGGTGAAGGTTTGCAATCCTTCTGTTATTATTTGTTTGTGGTTCTATGTGAAATCGTTAACCTCT
TTGCGTCTATGCGTCCTATTTTATTTATTTTTTTATAAAGGTATA
Right flanking sequence: Indices 52086 -- 52585
ATATAATACTAATATAGGCGTAACACTAAACTAAAACTTCCACATTCAGATATATATGGATATTG
GCAAACACGTTCAGTAAACTTACACTAACAAAGGAACACAAACACCAATCAGACAAATTACACCA
TTACATAAAAGAGAAAAGGACATACATAGGCTACCCAATCGTGCCGAGATTCACTAGGCTTGGAG
ACCTTAAGGAGGGGGGACTGCCAATCCTCAGAGAGCTTCGCCAACAGAAAAAAAACACTCCCACT
ACTAAGAACACCATAAGAAGACCTCATAAACAAGACAGCAAATTACAGGGGAAAGAGTCACTACT
TTTTCAGTCTCCCGGTCTCTGAGGGAACCGCACAATGAGCGCTTGCCTTTCTTCGAGCAGCGCCC
TCTTCCTGTTTTTGAGAGTGAAAATGGGGTTCTGGAGAAATGTCATATGATCCCGTATGATAATG
GGATCGAGAGCAGTAGGCTTAAGTAGAATCTTGACTCAGTCTAAC
Found at i:52101 original size:17 final size:16
Alignment explanation
Indices: 52048--52093 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
52038 TTTATAAAGG
52048 TATATATAT-ATATTAT
1 TATATATATAATA-TAT
*
52064 TATATATATTAGTATAT
1 TATATATA-TAATATAT
52081 TATATATATAATA
1 TATATATATAATA
52094 CTAATATAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 12 0.46
17 12 0.46
18 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
TATATATATAATATAT
Left flanking sequence: Indices 51548 -- 52047
GATAGATATTCTATGCATCTATGCAATTAGCAGTTGCTACTGCGCATTACTCACGACGTGGATGA
TAACCCTAACTGTCCCCTTATAGTGGATCGCGGGCTTTTCGGCTTGAAGTTTTGTAATCAATGAA
GTCCTGTCATGAAAAGAGGAAGTGTAACCTAATACAGAGACTTGTTGCGCACTTATTGAGTCGCT
GCTCAAATTGGTTGTGTGTGGTTATGACCTAAACTGCATAAAAACGATCGTTCTAGGCGCATTTA
AAAGCCTTTAAAAATAAAATGGTTTTTTTTCTCCTGTCTCATAATTCCGGTTTACTTTCAGTATG
GGATCTTTATTTCTACTATTTTGTTTAAGTCTTTCTCGGTGTCCGGCTTGGGTTCGGGTTTGTCT
GCTTTGGTGAAGGTTTGCAATCCTTCTGTTATTATTTGTTTGTGGTTCTATGTGAAATCGTTAAC
CTCTTTGCGTCTATGCGTCCTATTTTATTTATTTTTTTATAAAGG
Right flanking sequence: Indices 52094 -- 52593
CTAATATAGGCGTAACACTAAACTAAAACTTCCACATTCAGATATATATGGATATTGGCAAACAC
GTTCAGTAAACTTACACTAACAAAGGAACACAAACACCAATCAGACAAATTACACCATTACATAA
AAGAGAAAAGGACATACATAGGCTACCCAATCGTGCCGAGATTCACTAGGCTTGGAGACCTTAAG
GAGGGGGGACTGCCAATCCTCAGAGAGCTTCGCCAACAGAAAAAAAACACTCCCACTACTAAGAA
CACCATAAGAAGACCTCATAAACAAGACAGCAAATTACAGGGGAAAGAGTCACTACTTTTTCAGT
CTCCCGGTCTCTGAGGGAACCGCACAATGAGCGCTTGCCTTTCTTCGAGCAGCGCCCTCTTCCTG
TTTTTGAGAGTGAAAATGGGGTTCTGGAGAAATGTCATATGATCCCGTATGATAATGGGATCGAG
AGCAGTAGGCTTAAGTAGAATCTTGACTCAGTCTAACGACTTTGA
Found at i:57546 original size:18 final size:19
Alignment explanation
Indices: 57520--57556 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
57510 TGAAAACCGA
57520 GACTAAAGG-AGTGTACTT
1 GACTAAAGGAAGTGTACTT
*
57538 GACTTAAGGAAGTGTACTT
1 GACTAAAGGAAGTGTACTT
57557 CACAAGGGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.30
Consensus pattern (19 bp):
GACTAAAGGAAGTGTACTT
Left flanking sequence: Indices 57020 -- 57519
TTAAAGCCGGCCGGCCGATTTTAGAAAGAGAATCAACTAGTTTTGTTCTGATCTGAGTAGGCTCA
ACATAGGGAATACCCTAACCCTGGGAACCGGGGCCTGGCCATCCCATCCCGGTCTCCGCTCCTCT
CTAACTAACAGGAGAAGCGGAACATGTAGCTTTTCATCCTTGCTCGATCATCCTATCAGACATGG
TAACGGATTGAGTATCTCTCTTTCGGTAGCAGGTTTGACTGTTTGTGATCGAACAAAACAAAAAC
AAGATATATCGTAGTCAAGTAGAGCTAGACTGCATAATTGGCTTGTAGGAGAAAGAGTTGAAGGA
TTCTAGCCAAGAAAGACGGAGATGCAAGCTTTTTTTCTGTCTCTGCTATTGGATGTAATAGTGTG
GCACGCACTTTATCAACTCTAATGTTACCGGGTCTGCCTTATGTGATTTGAAAAGCTTTAGAAGA
AGGATTTCACCCAGTTTAAACTAAAATAAAGTAGTTGAAAACCGA
Right flanking sequence: Indices 57557 -- 58056
CACAAGGGGCTGTTGAGTAAGGGAGGGGTCGGTATACTAATATAAGTCTTTTTCATGGCAGGGAT
AGCACAAATAAGTAATGAAAGATCCATGTCCCCACCCTAGTTAGAAGAAATAAAGGGTATGCCTG
CGCGTAGAAGACCTAAAAAGCCTAAGCCTAATTCGGATCGGCCTATGAAAAGTAGTTCCCCGTGG
AAAGCGGGAGAGCTGTTGATGGAAGAGGAATCACCGGGTTGTTCGGTTCAATGGTTGGGAAGCTA
AGCTCCTTATAAAGGATTGACCGAGTACCCTTTTGTTTGCTTTTCCTGTTTGCTACCTAATAAGC
AATTGACTCTTTGTTTGCGATTCTTTCAAGGAAGGATCAATACGATCATATTGGCTCTATAGCAG
AAAAGGTCTGTCTTTCATGGACTAGATCCCAGCAGACAGCGATCTTCTCACTGAAAAACCAACGT
TTAACGAATCAGATGGGGGAATACATGAGGACCAGAAGATGCATT
Found at i:81203 original size:22 final size:22
Alignment explanation
Indices: 81171--81216 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
81161 TGTCGTCCAG
*
81171 CGGAGCTTAGAAGAAGGTGACT
1 CGGAGCCTAGAAGAAGGTGACT
81193 CGGAGCCTAGAAGAAGGTGACT
1 CGGAGCCTAGAAGAAGGTGACT
81215 CG
1 CG
81217 CGCAGACAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.37, T:0.15
Consensus pattern (22 bp):
CGGAGCCTAGAAGAAGGTGACT
Left flanking sequence: Indices 80671 -- 81170
TTCACTGTTGGCGGAAGCCAATGTCCCGGGGTCCCGGGGACTCATTCTGACTGAAACAAGGGGTG
GGTCTTTATCAACTTTCAAATCCAAGATTTCTGGGAAGAAAAAAGGCACTCTTCATTCTTCATTC
GAAACTCATGAATGTCGGGTCGGGGGTTTCTGCCTTGTTATAAAAAAGGGGAGTTGGGTAAAGAA
AACTCCCTCCTTGGACGAGCATGGGGCTTAGTCAAGTAGAACCGGGTTGCGCTGCTTGATGCTCC
GATCGAAAACAAATCAGTGGGGCCATGCCGGTACGACGGAATATGCGTTAGAAAGGTCAATCCCT
CCCCCCACCTTTATTATTAAGTCAAAAAAAAACCGGGCCGAACTTCTAAAAAGCAGCCCGCCCGC
TTCCATAGAACAATATCGTGGCAACGTAGACCTAAGTGAGTTTATTGGATCCTGGGAACCATCAC
AAGTACGGCCGGCCTTTATTTGAACGAGAATGCCGTGTCGTCCAG
Right flanking sequence: Indices 81217 -- 81716
CGCAGACAGCTGACTCCTTTTCAATAGAAAGGAATAGCCAAATCAACCCAGCTGGCTGGTCAATC
TTAGTGATCTTATCGGCCGGCAAACCGGAGACGGACGACCACGGTCCCGACCTTACCAGCATCGT
AGGTTTACTAATCAATGAACCCCCGAAACCTACTGTCTTTTCTGACAAAGTCAACAAAGCCGGAA
CAAACCGTCATGGTCACGACATGTTGTTGATATTGATGGAGTTGGAGGGAGTCAGAGACTACCAC
TGAATCCATCCATAAACCGTCACCCCGGTCACCTTCGTAACCAAAGCGTCACTTTTCCAAACCAA
AGGTTACCCGTCATCGAATCTCCAGTAGGGGGGGGGGCAAGGAGGAGCACGTAGGAATGCCAACC
ACTACATAAGCCCCTAGCGGCTGAGGCGAGCAGCAAGCGGGGGAGAGTCAAGTAAAGTACAACAA
CGTTGGGGTGGGACGCTAGTACTTAAACTAGGGTTGCTTCTTAGC
Found at i:109115 original size:28 final size:28
Alignment explanation
Indices: 109076--109130 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
109066 AGCAAGCCAT
*
109076 CCAATCTGGAAAGTCAGAAGTTCAGATC
1 CCAATCTCGAAAGTCAGAAGTTCAGATC
*
109104 CCAATCTCGAAAGTGAGAAGTTCAGAT
1 CCAATCTCGAAAGTCAGAAGTTCAGAT
109131 ATTGCACCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (28 bp):
CCAATCTCGAAAGTCAGAAGTTCAGATC
Left flanking sequence: Indices 108576 -- 109075
GGGAAGGTAGCTTCTTTCTATAGGCGACCGGTAGGTAGGCCGTGGGTGCAGAAGGAAAGCCGTAA
GGTTAGAGGTTAAAAAAAACTCTTTCTCGAAGTGCGTACTAGAAAGCTAGCGCCCTATTTTAATG
CTCTCTATCTTACCAATTTCTATCTAAGTTCCTCTAAAGAAGGTCTATCCCCTGAAAGCTAAGAT
CAATTGCTTGAGCTAGCTGTAGTCATTTACAGATTCTTTCTGACTGAGCGGCCTTCCTAAATAAG
AAATACGAGTTTGAGCTCGCATGACATATAGGTTCGCTCCGGGCTTGTAGAAGGTTGTTTTCAAG
TTTTGGGAGGGTCATCTAGAATTTCTCATTATGAGGCTGGATCGCCCATTTCGACCTAGAGATTC
TCACCCAGTCTCGCGCCATATGTACTGCTCCTCTCGGGTCACTTCAGCTCGGTCAAGTCTTTAGT
CTCGTTCCTTAAGTGACTCCGCGAAGCAAGCCAATAGCAAGCCAT
Right flanking sequence: Indices 109131 -- 109630
ATTGCACCGAACTATACGAGATCAAGGGCCCACGAAAGGTGACTTCGCTATGAGGCCCAGCCCCT
TCCCTAGCGAAGGAATCTCAGAATTGATTGCAATGAGTCCATTCGCAACGCCCGTTCAGTGATTA
CTTACGCACGCAATTAGTTGATCGAAATGTTTTATTTAAATTAACAAATGGAAATCATGTTCTTC
AAGTAAGGGAGCAGGCAGATCATCTATGTAATTAGTTCTAATTAGTTGATTAAAAAAGAGCGGAT
TCCATTAGTATTAGTAGAATGTGAGAAAGAAAGCGTTGAGCTGAGCTTTAAGCGCGAGAGGAGTG
CGCAGTAGATGAGGTCTAACTGTCCGAGTCCTTTCAGGCTTACTGAAGACTAAGCCAACGCAAGC
GCCTTATTTCAAAACATGGTTAAAGGATCAAGCCGCAAGATTCCAGGTCAACTTGACTTGGTACT
GATTCCGGGTAACCATAGAAAAGGAAGGGACGAAAGAGCTAAGCG
Found at i:121845 original size:14 final size:15
Alignment explanation
Indices: 121826--121865 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
121816 TGCAGTCCTC
121826 AGAG-AATAACTAGG
1 AGAGAAATAACTAGG
*
121840 AGAGAAAGAACTAGG
1 AGAGAAATAACTAGG
121855 A-AGAAATAACT
1 AGAGAAATAACT
121866 CTAGCAACTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.55, C:0.07, G:0.25, T:0.12
Consensus pattern (15 bp):
AGAGAAATAACTAGG
Left flanking sequence: Indices 121326 -- 121825
GATTGACTCTGGCAGCGGAAGCGAAGGAAGGATAAGCAATCGGCTGAATGATGGATCGATTTCCA
TCGTTGACTTCTAGTCTTCTATCGAAACAGAGCAAGTTTCATACTCCAGCCCCGGGGATTCCATT
TCGATCCGCCAGCCCAAATCTATCTAATAAGAGTCCTTACCCCGCATTCATCAATATCAATAAAA
GTAGCAGGCGTGAAGAGTCGTGAAGGTTTAGTATACTAACTTCTAGTTACCGCACAACGTCCTTT
CCTTCGGAACCTTGGAACTATGTATTGCAGTTGGCAGATCACAGAAGGAAGTCAATAGCATACTA
GAGTAGAGGGTAGGGGGGAAGGAACTGATTTAGCAATACAGCTAAACCACTAATTATCTATAATA
GGTGCCTATCTCTTTTCTTTTGTTACAGAATTAAAGAGTAAGGCATGAAAGATCAGAGAAAAAGG
AATCAGTCTTAGAAGTTCATAGACGGTTGGTTAAATGCAGTCCTC
Right flanking sequence: Indices 121866 -- 122365
CTAGCAACTGGGAAAGAGAACTCCTAAGAGTAAGAGCAGCCCTTCGTGTAGGAGGGTGTAGGAGC
GAAGCCACTCTTGCCCCTTCTTCCACTAGTCTTAGAGATAGGAACTGGGAAAGAGTCACCGAGAA
AAGGCATGAAGGGGCTTACTAATAATAAAGATAAGGCATGCATGAAGGAGGTGACTCAGGAATGA
AGGAGCCTAGTCTATTTGAGGCGGGATGCCCAAGAATAGAAGTCGCCATATGCCGAAAATCGTCT
TCTGTGATGTCAGGGAGAAATCGTCTGCTCACTTGCGACAAGAGGTTTTCCATGGATTCTAGCAC
AACCGATTCGATGTCAAAGGATAAAGGAAAGGCGACAAAAGCTCTTATTCCAACAAGCCCAGAAA
ATTAAGAGGATAAATGGGCTAAATTCTTACCGATGATATTACCAGTTATTCCGACAACAGCTTAT
GATATCACCCTCGGGTCACTCCCTAAAGAGTTAAATCCATTCCTT
Found at i:143819 original size:21 final size:21
Alignment explanation
Indices: 143789--143828 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
143779 TTTTTAATAG
* *
143789 ATAAATAAGGGATTCTCTTCA
1 ATAAAGAAGGAATTCTCTTCA
*
143810 ATAAAGAAGGAATTGTCTT
1 ATAAAGAAGGAATTCTCTT
143829 ATCATATATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (21 bp):
ATAAAGAAGGAATTCTCTTCA
Left flanking sequence: Indices 143289 -- 143788
AACCACCCCTATTCTCGCAACAAGCGACCCGTTTCTCCTTTTAGAAAGTCGGCTGTTCTAGCGAG
CCCCGCTATTTCAGAGAGTGGAAGGTCCTCTCTGTCAGAGGCGACCGGGGGTGCTGCCTCGAAGA
ACTGCATGACCTACGATACCGAAGGCCTTTCCTCATTTAAGATATTCTTTCGCGACAATAAAATA
AGAAGAAGAGGAATAGTGATAAATGAGCGGAGGCGCTAGGAAAAATAATAGGATTTAACAGCTAA
ATAAGCTCCTAAATGCAGCCGTGATCAACTATACGATAGCACCTGATGCGATCGGACCGGATCTA
AGGCCCAAGTAGCCCCCTGTACGAGAAATGGTTATGAACTGACAAGGAAACCTCCTTCCGCGGAA
CACCATCTTAAAGAGTGAAGTCAACATAGTCGGCATCAAGACCTGCATTCTTTTATTTTTTCTTC
TTTTCCTTCGGAACCTCATTTCTTTTGATATTTTTTTTTTAATAG
Right flanking sequence: Indices 143829 -- 144328
ATCATATATATGATCTTTTTTTTTAGTTGGTACATGTAGTGATATAAACTCTATAACGCTAATTT
AGACGAGATTCTTAAAAAAGGCGACGATTTCTTATTGTTCTGACAACAGAAAGATAAAGCCATAT
ATATTCTTCTATAAATAATATAATAATAAAGGGTGTTGGTGAAAGCGGAAAGGTTATTTTTCTTC
CCCATTTCCATCATATGATGGGCTAAAACTTCCGCTTCCATCGGTTGCGAGGAGCTCTTTTTATT
AGTGTCCCCTTCAAATTGATTGAGACAAGCAAGCCTAAACCGAGAGTCCCACAGGGTTGACTTTT
TCCTCGAAAAAGGACTTTTTTTTTGATTCACCGACAAGCGATAGCCAAGCTAGATGAGAAATGAA
GATAGGGAATCGGCCGCATCAACTCTTTCTGGGTCGTCCAAAGAAGCTTATCCATAGTACGCAAA
GAAAGGAACCGGCACCATTAGATCGAATTTTCAGTAGATCGAGTG
Found at i:164631 original size:20 final size:20
Alignment explanation
Indices: 164582--164634 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
164572 TGAAAGGAAC
*
164582 TGCAAACTACGGCTTTTCAG
1 TGCAAACTACGGCTTTTCAA
* **
164602 CGCATGCTACGGCTTTTCAA
1 TGCAAACTACGGCTTTTCAA
*
164622 TGCACACTACGGC
1 TGCAAACTACGGC
164635 CGAACTCCGT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (20 bp):
TGCAAACTACGGCTTTTCAA
Left flanking sequence: Indices 164082 -- 164581
TTAAACAGCAGCGCTTGGAGGTTTTTTTCGAGGAAGACAGAGACAAAGAGCCAGAAGCTATGGAG
AAAGAATGGGATTTGGTTACGCTATCTGACGGAAAGATCGAGGTAACTGAAGAGCAATCCGCAGG
AAGTGCACTATGTCCCAGATAAGGCCGAAGGTCCAAGACAGAGTTGTAGGTAAACTCGTAAGAAA
GAATTGGTCAACAAGGTTCGCCCTTACTTAATCGGCAGAGAGTTTATTTGCTGAATCAATCTCTG
TCACCTGGCACTAAAGTCGATCTTAGGGAGTCAATAGGTGTTCCAAAACTAAACAGTATAGCTTA
TTAGCTCGTCCCGTATCTTCAGTAGACAAGACAAGAGGCCGGTCAAGCAAGTCTGTTGGCAAGCC
TGTAAACTAAGCTAGACGACTACTCCTTTCTTTCTTAGCCTATAACGACGTTATCAATCCCTATT
TTTTCGGATATCTGTCTTCATAAGCTACTCTTGAATGAAAGGAAC
Right flanking sequence: Indices 164635 -- 165134
CGAACTCCGTTTGCTGGATCCGGCTTTCTTTGGCATACAGCACTGTGTATGACTTAGGTAACACA
TCAGTTACCACGGCACTCTTTGTCTTCAACGCAAGCGCCTTGACGAGGGGAAAGAGCCCTTTTCA
TATAACTAAGAAAGAGACCCACAGTCTCGTAGCGACCGTTAAGCTCGTAGCAAGAAATAAGGAAC
CATTGCGGATGATTTAGATAGAGGGCGCAGGCAGGTGTAGGCAGAAGCTTTCTGAGTCGGGGAGT
TAGAGACCTTGAAGGTTACCCGAGACTAGCCTTTTTAGGTTTCCGGTATGCGTACCACCGAGGTC
TTGTGAAGAGCCGGGTCCATAAGCCAATTATAAAAACTGTCTTGGTGCAAGGGATCAACAGGACA
CTAACCCATTCCTCTTCTCTTTGCGGAAACGGGAACGGGAATAATGAATGCATACTCGCATGGAT
GTCCTTGCTTGTAGAATGCACGTGGGAGAAGCGATAGGCGACACC
Found at i:191024 original size:2 final size:2
Alignment explanation
Indices: 191017--191058 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
191007 TTAGGTGGAT
* * *
191017 TA TA TA TA TA TC TA TA TA TA GA TA TA TA TA GA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
191059 GGGAAAAACC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Left flanking sequence: Indices 190517 -- 191016
TAGCCACTGAGCTGCCGAACTTCGGAAGCGACAATCTCTTGAGTTCACATTCTAAGGAACCTTCT
GAAGAGCTAATTCCTAACTATTTAAGGCTAAGGTTAGAAGAGCTGCTAAGCGCTACTACAAATGC
CTTGGTCAGATTCGGGCTGCCCTATTGAGTAATGGGGAGCAATTCATTACTACTTAGTAATGAGC
TGTTGAGGGAACCTTCTAGCGTCATTCTATAGAGTTTGGGATAGCAATGGTTGAGACCTGCGGCC
TTTTCTTTGGCTAAGGTTTGACAATCTAAGGTTAGGTAGCGGAAATCACTCTATAGACAGAAAAT
AGAAAGAAGAAGGTAGATCTAAAGTAAGTTCCATAAAGGGATGTATGCCAAGCTATCATATAGTT
ATAGCCATCAAAAAAAAAAAGTTGACCTCTGAGGAGGTAACCACCTTCCTGACGGAACGGGTTCA
ATGGAAAAAAAGTACACCAAGCAAACCTTTAATACTTAGGTGGAT
Right flanking sequence: Indices 191059 -- 191558
GGGAAAAACCCTAATTCCATAGTTCAATGGGTACGGGGATTGAACCCGCGCGTGGTGGATTCACA
ATCCACTGCCTTGATCCACTTGGTTACATCCGCCCCTACCCCCGCGCACTCGTTTCAGTCTCTAT
CTACGATCAGATCCTTTCTGGACCCTCCCTATGACCGCTATCAAAGAGAAGCTTTTTCCGATAGT
TGCAAATCTATTGTTTGTTGTGTTTTTTGGAATTAGGGGAAGCTTTGCTTCAACAAGCAAGTAGA
AGCTTCCTGGCAACGCTTCAAACAAAGAGGTTGGGCTGTTCACTTCATTGATTTGACTCCACTTT
ACACATTAGTTGATACGGGCCGGGCGGCTTATTGATCAAACAAAGGAAGGCTCGTTTAGTAGACA
GCGAGCAAGCAGCAAGCGTAGGCAACCCTAGTTTAAATAAGTTTGGATAGTAGGGTTATTAAACA
AGTTTATCTATTAAACAAGTATATCTATTTAAAGAGACATAAGAA
Found at i:191527 original size:17 final size:17
Alignment explanation
Indices: 191505--191542 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
191495 ATAGTAGGGT
*
191505 TATTAAACAAGTTTATC
1 TATTAAACAAGTATATC
191522 TATTAAACAAGTATATC
1 TATTAAACAAGTATATC
191539 TATT
1 TATT
191543 TAAAGAGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (17 bp):
TATTAAACAAGTATATC
Left flanking sequence: Indices 191005 -- 191504
ACTTAGGTGGATTATATATATATCTATATATAGATATATATAGATATATATATAGGGAAAAACCC
TAATTCCATAGTTCAATGGGTACGGGGATTGAACCCGCGCGTGGTGGATTCACAATCCACTGCCT
TGATCCACTTGGTTACATCCGCCCCTACCCCCGCGCACTCGTTTCAGTCTCTATCTACGATCAGA
TCCTTTCTGGACCCTCCCTATGACCGCTATCAAAGAGAAGCTTTTTCCGATAGTTGCAAATCTAT
TGTTTGTTGTGTTTTTTGGAATTAGGGGAAGCTTTGCTTCAACAAGCAAGTAGAAGCTTCCTGGC
AACGCTTCAAACAAAGAGGTTGGGCTGTTCACTTCATTGATTTGACTCCACTTTACACATTAGTT
GATACGGGCCGGGCGGCTTATTGATCAAACAAAGGAAGGCTCGTTTAGTAGACAGCGAGCAAGCA
GCAAGCGTAGGCAACCCTAGTTTAAATAAGTTTGGATAGTAGGGT
Right flanking sequence: Indices 191543 -- 192042
TAAAGAGACATAAGAATATGAATAGATAATATACAAGAGCTACAAAGTATAGTTGGCATTAGCAT
TTTATTTCGGAGGGAAGTTTAAGGTATTGGGACACAGAGGGAATAGAACCTTCTTGTCGACTCAT
AGCTCCCAGACTCCCTCCCATTCATTCCCTTAAACAAACGGCAAACGGTAAAGGTGACGTGCAGA
CTTTAAAATATATCCGAATAGAATAAGGAGGCGGGCAAATCTGTGCGAAGAAGGATAGAAAGCAA
GACGAAGAATTTTCCACCGAATCGTTCACAGAAGCTAGGCCAGGCCCTGATGGGTCTGCTCGTTT
GGAAGAACGATCAAAACCGACGGGATCGGCTCACTACTCCACATGTTCAGAGTCCTCTAAGTCAG
ACTTATAACCACCAAAATGGGATTTCATTACTCAGGACACGAAACCGGAGTCGAGAGACTGACCC
CCCTCCTACTTCCCCGTCCGATCCTCATACCTGGGGACCTTCCAC
Found at i:203983 original size:27 final size:27
Alignment explanation
Indices: 203925--203983 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
203915 CCCTCCAAGG
*
203925 GGAGGCGCATCCGACGGTCGCTTCCCC
1 GGAGGCACATCCGACGGTCGCTTCCCC
* *
203952 AGAGGCACATCCGGCGGTCGC-TCCTCC
1 GGAGGCACATCCGACGGTCGCTTCC-CC
203979 GGAGG
1 GGAGG
203984 AACCGGTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 3 0.11
27 24 0.89
ACGTcount: A:0.14, C:0.37, G:0.36, T:0.14
Consensus pattern (27 bp):
GGAGGCACATCCGACGGTCGCTTCCCC
Left flanking sequence: Indices 203425 -- 203924
GGTTAACGATTTCACATCTACTCTTTGCCGATGATACAATAGTATTCACAAATGGCAGCTTGTAG
TCCCTTCAAAAACTCATGGATTTATTTCCAGGAAGATTATCAGCTTGCATCTGGTCAAAGAATCA
ATAAAAGCAAGCAAGAGTGGCTTCCTTCCTTTTATTTTAAGTCGTGGAGCTTCTCAAAGTAGGGA
GGACATCATGCTAATGCACTAGGTCTAAATGGGAAATTCCTTCCTATTACATACCTTGGGGTACC
CTTTTTGATGGACATTGCACTGCAGCTATTTAAAATGAAAGATTTGGTGGAAAGATTCGCTCGAG
GATTGATAGTTGGAGTGCCAAGCTCTTAGGAGTAAGATGGACTCTTATATAGAGTGTTCTCTCTT
CGATTCCCCTCTATACTCTTGCTGCTCTTTCCCCTCCTCATTTAAACGAAATTATAACGAGCTCG
TCAAATCCTAACGTTTCGGAACCTAAGCTTTTGCTCCCTCCAAGG
Right flanking sequence: Indices 203984 -- 204483
AACCGGTATTACAGATTCCCGACCCTTTTTCCAAACGACGACCTTTTTCCGAACTTAGGCAATCC
GGATCCAATTCCGGATGTGGATGTGGACGCCCTTATCGAAGCTGCCTATGATAACATACATTTTG
CGATTGAACAAATACATTTAGTATTGTTCACCTTTTATGCCTGAATGGATATTTATTCGTGAGAC
AACTAGGTTCTCTCTACCTACTTAAAGAAGAAAACGATCTTGAATATCTCAATGAGGTATTCTAC
GATCTATTAGCTTTTGGTGAACACTTGGAGTTCTTCCATTTTTTGGAAGACTGTTTACAACAACA
ATGGATTTTCGTGTGAAAAATGGGTAGGGATCGAATTTCAATTGCTTTAGCGGGAGCTGGTGTTG
CAACGTCTCTTTTGTTCTTCTGAGTCTTTTTTTACCATGAGCGAGGGTACTCCATTGCGTAGTTG
AACCTTCAGCACCGGTGGGAGGAGGCTCTGAAGTCAGACTGGAGG
Found at i:211671 original size:20 final size:20
Alignment explanation
Indices: 211646--211691 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
211636 ATCTAAGCTC
*
211646 CGGCTTTTCAGCGCGCACTA
1 CGGCTTTTCAGCGCACACTA
*
211666 CGGCTTTTCAGCGCACGCTA
1 CGGCTTTTCAGCGCACACTA
211686 CGGCTT
1 CGGCTT
211692 ACGCAGTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.13, C:0.35, G:0.26, T:0.26
Consensus pattern (20 bp):
CGGCTTTTCAGCGCACACTA
Left flanking sequence: Indices 211146 -- 211645
GAAGATTCTAGAAGCAAGCTACGCTACCTTCTGGCTAGCTCGTGCAATCTTAGAAAAATTCCTTC
GCGCTTAGCTTAGTAAGCTAGCTTGGTAAGCTAAGCAAGCCTGGTTCTCCGGGCATTATGGTAGG
ACGTGGATCGATCATGACGAGAATGGACTTCTCCGTAATGTAATGGTTTAGTCACGGTCCAGGGG
TTGGGTCTCGACCAACCAGACGAAGGAGATATGAATTCCATTCAGGCAGGTAAGGAAGGGGGGCT
TGGCTTGACCGTGTGTTCTCTCTCTCCTGGTCAGGTCGGAGGCGAAGACTGGCAAAGTTCATCAT
TCAGCGGTGGGGTGTTCATAGAAAGGAGAAAGGAAGGCGTCGCCCAACGAGTGGCGGAGATGGAC
TTGGATGCTGGGGAGATCCATAGATTTGGATAGAGTCTCGCTCATAGAAGAAGAGTACGCGCGCT
AGCTTCAAAACAACAGGGCGCGTCAGAGAAGGAAAATCTAAGCTC
Right flanking sequence: Indices 211692 -- 212191
ACGCAGTGAATCGGATCAGATTTGACTTCGGGCAACCAACCCGGCACATCCAATTCCGATCAACA
ACAGGGAGGTATGGCTGAGTGGCTTAAGGCATTGGTTTGCTAAATCGACATACAAGAAGATTGTA
TCATGGGTTCGAATCCCATTTCCTCCGGCACGGAAGTGGAACGGGCGGGCGAAACGAAATGACGT
GAGATAAAACTTGGAACCCGGAGGACAAGCACTACTTTACTTAGTGACTAGGAGCGGAGAGCCTC
TTTCTTGTTCTTGGTGGCGTCTATAGCGAAGAAGACCTGACCGAACGAGGTTGAATTTCTTCACC
CTGGCCGGCTCTCGGTTCTTGAGCAAGCTCCTCCACTGCGGGTAGGGCGCTATTTTATTTGATGA
AGAAAATCTACTTTAGGAAAGTGGTTCAGGTAGCTCAGTTGGTTAGAGCAAAGGACTGAAAATCC
TTGTGTCAGTGGTTCGAATCCACTTCTAAGCAGGAAACGTAGCCG
Done.